Predicted Trait | |
Reported Trait | Immature reticulocyte fraction |
Mapped Trait(s) | Immature Reticulocyte Fraction Measurement (EFO_0009253) |
Additional Trait Information | http://ipgs.mit.edu/tanigawakellis2023/INI30280 |
Score Construction | |
PGS Name | INI30280 |
Development Method | |
Name | snpnet |
Parameters | inclusive PGS |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 16,307 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000502 |
Citation (link to publication) | Tanigawa Y et al. AJHG (2023) |
Ancestry Distribution | |
Score Development/Training | |
PGS Evaluation |
Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) | Phenotype Definitions & Methods | Age of Study Participants | Participant Follow-up Time | Additional Ancestry Description | Additional Sample/Cohort Information |
---|---|---|---|---|---|---|---|---|
— | 310,754 individuals | European, South Asian, African unspecified, Other admixed ancestry | UKB | — | — | — | European, South Asian, African unspecified, Other admixed ancestry | — |
PGS Performance Metric ID (PPM) |
PGS Sample Set ID (PSS) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
Classification Metrics | Other Metrics | Covariates Included in the Model |
PGS Performance: Other Relevant Information |
---|---|---|---|---|---|---|---|---|
PPM019069 | PSS011143| European Ancestry| 64,816 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.10325 [0.09891, 0.10759] PGS R2 (no covariates): 0.09279 [0.08863, 0.09695] Incremental R2 (full-covars): 0.09226 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019070 | PSS011100| European Ancestry| 2,768 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.09801 [0.07746, 0.11857] PGS R2 (no covariates): 0.09403 [0.07381, 0.11425] Incremental R2 (full-covars): 0.09203 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019071 | PSS011111| South Asian Ancestry| 1,393 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.06095 [0.03744, 0.08446] PGS R2 (no covariates): 0.05417 [0.03184, 0.07649] Incremental R2 (full-covars): 0.05046 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019072 | PSS011152| African Ancestry| 1,124 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.04778 [0.02442, 0.07113] PGS R2 (no covariates): 0.03953 [0.0181, 0.06096] Incremental R2 (full-covars): 0.0407 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PPM019073 | PSS011170| Multi-ancestry (excluding European)| 7,574 individuals |
PGP000502 | Tanigawa Y et al. AJHG (2023) |
Reported Trait: Immature reticulocyte fraction | — | — | R²: 0.10912 [0.09624, 0.12201] PGS R2 (no covariates): 0.08182 [0.07032, 0.09332] Incremental R2 (full-covars): 0.08036 |
age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) | — |
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
---|---|---|---|---|---|---|---|---|
PSS011143 | — | — | 64,816 individuals | — | European (white British ancestry) |
— | UKB | — |
PSS011111 | — | — | 1,393 individuals | — | South Asian | — | UKB | — |
PSS011152 | — | — | 1,124 individuals | — | African unspecified | — | UKB | — |
PSS011100 | — | — | 2,768 individuals | — | European (non-white British ancestry) |
— | UKB | — |
PSS011170 | — | — | 7,574 individuals | — | East Asian, Other admixed ancestry | East Asian, Other admixed ancestry | UKB | — |